In the current release, when Pads are removed, the Trace to Pad spacing becomes the Trace to Hole spacing.
In the upcoming release, additional controls have been added for Drill Hole to Copper tolerances and spacing.
Thank you for your reply Vern.
No workaround at the moment?
Which upcoming release?
I just installed 2.1.3 and wanted to use the internal layer overrides.. they work great to remove unused pads.
I still haven't found a way to reduce the clearances on the plane layers copper to drill.
Am I missing something?